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[Rcpp-devel] Unable to install RcppArmadillo from CRAN or from SVN archive on Ubuntu 10.10

8 messages · Dirk Eddelbuettel, Conrad Sanderson, Jan de Leeuw +1 more

Dirk Eddelbuettel
#
On 29 April 2011 at 22:56, Conrad Sanderson wrote:
| Sorry, I don't know what's going on.  As far as I know, the structure
| "arma_version" (as defined in the file
| "include/armadillo_bits/arma_version.hpp") is following the C++
| standard.  Please double check and let me know if it's not right.
| 
| If the structure is giving trouble and it's not really used in Rcpp,
| perhaps it's best just to remove it ?

Thanks for the feedback.  And yes, by not referencing it from
src/RcppArmadillo.cpp  we could avoid the issue---and Jan and Doug can try
commenting this out in the short function armadillo_version to avoid the
linker issue, at least for a test.

We may well have to consider removing this code bit (which we don't really
need any more and only needed in the past) but it feels wrong to declare
defeat to the compiler this way.

Dirk

 
| 
|
| On 29 April 2011 22:35, Dirk Eddelbuettel <edd at debian.org> wrote:
| >
| > (Conrad, This started as this thread
| > ? ?http://thread.gmane.org/gmane.comp.lang.r.rcpp/1877
| > ?which picks up the issue first reported by Jan regaring arma_version not
| > ?being found by the linker and which you commented on so colourfully a few
| > ?days ago.)
| >
| >
| > On 28 April 2011 at 13:38, Jan de Leeuw wrote:
| > | And I have armadillo-1.2.0 compiled from source on the Mac in /usr/local
| > |
| > | But removing the include and lib files does not help
| >
| > So just as a reference point, I did have Ubuntu's libarmadillo(0,-dev-doc)
| > installed but both before and after purgeing them, I can do 'R CMD check
| > RcppArmadillo' just fine against the SVN sources. ?Dito for R CMD INSTALL.
| >
| > So I don't what's going on -- there should not be an issue building this.
| > And on my end (and Romain's for that matter) it worked before and after the
| > suggested by Conrad to use arma::version::major etc directly.
| >
| > So I really don't know
| >
| > ? a) what is going on with Doug's setup as I use a very similar machine /
| > ? ? ?setup on my Ubuntu box --- but then Doug unfortunately had build issues
| > ? ? ?with related code on his box but not on mine, and
| >
| > ? b) what is going on Jan's Mac -- other than Conrad's earlier colourful
| > ? ? ?remarks about maybe something being fishy with the OS X compiler, but
| > ? ? ?that is just a guess too.
| >
| > Also, a simple check (see below) builds fine here. The RcppArmadillo package
| > really does nothing much different than this check: access the elements of
| > that struct.
| >
| > So I remain rather puzzled. ?One local build issue I could live with, but
| > that both Doug and Jan have issues is a little strange. ?But as I said:
| > nothing I can replicate at my end. This should just work.
| >
| > Dirk
| >
| >
| > edd at max:~/svn/rcpp/pkg/RcppArmadillo/inst/include$ cat /tmp/quickCheck.cpp
| >
| > #include <armadillo>
| >
| > int main(void) {
| > ?std::cout << "Seeing " << arma::arma_version::major
| > ? ? ? ? ? ?<< "." << arma::arma_version::minor
| > ? ? ? ? ? ?<< "." << arma::arma_version::patch << std::endl;
| > }
| > edd at max:~/svn/rcpp/pkg/RcppArmadillo/inst/include$ g++ -I. -o /tmp/quickCheck /tmp/quickCheck.cpp
| > edd at max:~/svn/rcpp/pkg/RcppArmadillo/inst/include$ /tmp/quickCheck
| > Seeing 1.2.0
| > edd at max:~/svn/rcpp/pkg/RcppArmadillo/inst/include$
Jan de Leeuw
# 
On my machine RcppArmadillo compiles/links fine with

deleeuw at cuddyPro:~/Desktop/ > /usr/local/bin/g++ -v
Using built-in specs.
COLLECT_GCC=/usr/local/bin/g++
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin11/4.7.0/lto-wrapper
Target: x86_64-apple-darwin11
Configured with: ../gcc-4.5-trunk/configure --build=x86_64-apple-darwin11 --host=x86_64-apple-darwin11 --target=x86_64-apple-darwin11 --enable-languages=c++,fortran --prefix=/usr/local --with-gmp=/usr/local --with-mpfr=/usr/local --with-mpc=/usr/local
Thread model: posix
gcc version 4.7.0 20110424 (experimental) (GCC) 

but it compiles but refuses to link with

deleeuw at cuddyPro:~/Desktop/ > /usr/bin/g++ -v
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /var/tmp/llvmgcc42/llvmgcc42-2335.11~3/src/configure --disable-checking --enable-werror --prefix=/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --enable-llvm=/var/tmp/llvmgcc42/llvmgcc42-2335.11~3/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.11.00)

It also works fine with

deleeuw at cuddyPro:~/Desktop/ > /usr/bin/gcc-4.2 -v
Using built-in specs.
Target: i686-apple-darwin11
Configured with: /var/tmp/gcc/gcc-5666.3~168/src/configure --disable-checking --enable-werror --prefix=/usr --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin11 --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 --target=i686-apple-darwin11 --with-gxx-include-dir=/include/c++/4.2.1
Thread model: posix
gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)

So it may be the LLVM g++ compiler (note that this is a developer version which has not been released yet, comes with Xcode 4.1) or an unfortunate interaction of that compiler with libraries in /usr/local. For now, I will rebuild my R with clang, gfortran-4.7.0, and the stock (non-LLVM) g++ compiler from Apple.
On Apr 29, 2011, at 06:18 , Dirk Eddelbuettel wrote:

            

      
      
      
    

        
===
Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics;
Director: UCLA Center for Environmental Statistics (CES);
Editor: Journal of Multivariate Analysis, Journal of Statistical Software;
US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw at stat.ucla.edu
.mac: jdeleeuw ++++++  aim: deleeuwjan ++++++ skype: j_deleeuw
homepages: http://gifi.stat.ucla.edu ++++++ http://www.cuddyvalley.org
 -------------------------------------------------------------------------------------------------
          No matter where you go, there you are. --- Buckaroo Banzai
                   http://gifi.stat.ucla.edu/sounds/nomatter.au                                  
 -------------------------------------------------------------------------------------------------

  
  


  


      

    

    

      
      

        


  

        

      Conrad Sanderson
    

    

      
      #
    

  


  

      
On 29 April 2011 23:40, Jan de Leeuw <deleeuw at stat.ucla.edu> wrote:

            

      
      
      
    

        
I suggest filing a bug with Apple.  The LLVM compiler is rather fresh,
and it appears that it's still not ready for production use.

Perhaps Apple is doing an elaborate public beta test with this
developer version.  If so, one has to wonder whether Apple internally
lacks sufficiently varied test cases.

  
  


  


      

    

    

      
      

        


  

        

      Douglas Bates
    

    

      
      #
    

  


  

      
Yesterday I upgraded to Ubuntu 11.04 for which the default g++ version is 4.5.2

I rebuilt R-devel and R-patched from the sources and things changed --
R-devel CMD check Rcpp now fails at a different point.  This time it
doesn't segfault but it does produce results that are different from
the reference values.  All the failed tests are in tests of sugar
constructions.  I enclose the Rcpp-unitTests.txt file.

 RcppArmadillo still fails to load because of
arma::arma_version::major (and minor and patch) being undefined in the
shared object.

Later today I will use g++ with the -E option to see if I can track
why armadillo_bits/arma_version.hpp is not being included.o

        
On Fri, Apr 29, 2011 at 8:40 AM, Jan de Leeuw <deleeuw at stat.ucla.edu> wrote:

            

      
      
      
    

        
-------------- next part --------------
RUNIT TEST PROTOCOL -- Fri Apr 29 09:12:16 2011 
*********************************************** 
Number of test functions: 326 
Number of errors: 0 
Number of failures: 8 

 
1 Test Suite : 
Rcpp unit testing - 326 test functions, 0 errors, 8 failures
FAILURE in test.sugar.asvector: Error in checkEquals(res[[2]], as.vector(outer(1:4, 1:5, "+"))) : 
  Mean absolute difference: 5.5
FAILURE in test.sugar.beta: Error in checkEquals(fx(10:6, 5:1), list(VV = beta(10:6, 5:1), PV = beta(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
FAILURE in test.sugar.choose: Error in checkEquals(fx(10:6, 5:1), list(VV = choose(10:6, 5:1), PV = choose(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
FAILURE in test.sugar.diag: Error in checkEquals(res, target) : 
  Component 3: Mean absolute difference: 5
FAILURE in test.sugar.lbeta: Error in checkEquals(fx(10:6, 5:1), list(VV = lbeta(10:6, 5:1), PV = lbeta(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
FAILURE in test.sugar.lchoose: Error in checkEquals(fx(10:6, 5:1), list(VV = lchoose(10:6, 5:1), PV = lchoose(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
FAILURE in test.sugar.matrix.outer: Error in checkEquals(fx(x, y), outer(x, y, "+")) : 
  Mean absolute difference: 4.5
FAILURE in test.sugar.psigamma: Error in checkEquals(fx(10:6, 5:1), list(VV = psigamma(10:6, 5:1), PV = psigamma(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ



Details 
*************************** 
Test Suite: Rcpp unit testing 
Test function regexp: ^test.+ 
Test file regexp: ^runit.+\.[rR]$ 
Involved directory: 
/tmp/Rcpp.Rcheck/Rcpp/unitTests 
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.DataFrame.R 
test.DataFrame.AttributeProxy: (2 checks) ... OK (0.01 seconds)
test.DataFrame.CreateOne: (1 checks) ... OK (0.01 seconds)
test.DataFrame.CreateTwo: (1 checks) ... OK (0.01 seconds)
test.DataFrame.CreateTwo.stringsAsFactors: (1 checks) ... OK (0 seconds)
test.DataFrame.FromSEXP: (1 checks) ... OK (0 seconds)
test.DataFrame.SlotProxy: (2 checks) ... OK (0.02 seconds)
test.DataFrame.index.byName: (2 checks) ... OK (0 seconds)
test.DataFrame.index.byPosition: (2 checks) ... OK (0 seconds)
test.DataFrame.string.element: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Date.R 
test.Date.components: (1 checks) ... OK (0.01 seconds)
test.Date.ctor.int: (3 checks) ... OK (0.01 seconds)
test.Date.ctor.mdy: (1 checks) ... OK (0 seconds)
test.Date.ctor.sexp: (5 checks) ... OK (0.01 seconds)
test.Date.ctor.string: (2 checks) ... OK (0 seconds)
test.Date.ctor.ymd: (1 checks) ... OK (0 seconds)
test.Date.getFunctions: (3 checks) ... OK (0.01 seconds)
test.Date.operators: (1 checks) ... OK (0 seconds)
test.DateVector.operator.SEXP: (1 checks) ... OK (0 seconds)
test.DateVector.wrap: (1 checks) ... OK (0 seconds)
test.Datetime.fromString: (1 checks) ... OK (0 seconds)
test.Datetime.get.functions: (1 checks) ... OK (0 seconds)
test.Datetime.operators: (1 checks) ... OK (0 seconds)
test.Datetime.wrap: (1 checks) ... OK (0 seconds)
test.vector.Date: (1 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Function.R 
test.Function: (7 checks) ... OK (0.01 seconds)
test.Function.binary.call: (1 checks) ... OK (0 seconds)
test.Function.env: (3 checks) ... OK (0 seconds)
test.Function.unary.call: (1 checks) ... OK (0 seconds)
test.Function.variadic: (2 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Language.R 
test.Formula: (1 checks) ... OK (0 seconds)
test.Formula.SEXP: (5 checks) ... OK (0 seconds)
test.Language: (7 checks) ... OK (0.02 seconds)
test.Language.binary.call: (1 checks) ... OK (0 seconds)
test.Language.fixed.call: (1 checks) ... OK (0 seconds)
test.Language.function: (1 checks) ... OK (0 seconds)
test.Language.in.env: (1 checks) ... OK (0 seconds)
test.Language.inputoperator: (1 checks) ... OK (0 seconds)
test.Language.push.back: (1 checks) ... OK (0 seconds)
test.Language.square: (2 checks) ... OK (0 seconds)
test.Language.unary.call: (1 checks) ... OK (0 seconds)
test.Language.unary.call.index: (1 checks) ... OK (0 seconds)
test.Language.variadic: (2 checks) ... OK (0 seconds)
test.Pairlist: (8 checks) ... OK (0.01 seconds)
test.Pairlist.insert: (1 checks) ... OK (0 seconds)
test.Pairlist.push.back: (1 checks) ... OK (0 seconds)
test.Pairlist.push.front: (1 checks) ... OK (0 seconds)
test.Pairlist.remove: (3 checks) ... OK (0 seconds)
test.Pairlist.replace: (1 checks) ... OK (0 seconds)
test.Pairlist.size: (1 checks) ... OK (0 seconds)
test.Pairlist.square: (2 checks) ... OK (0 seconds)
test.Pairlist.variadic: (2 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Matrix.R 
test.CharacterMatrix: (1 checks) ... OK (0 seconds)
test.CharacterMatrix.column: (1 checks) ... OK (0 seconds)
test.CharacterMatrix.diag: (1 checks) ... OK (0 seconds)
test.CharacterMatrix.row: (1 checks) ... OK (0 seconds)
test.GenericMatrix: (1 checks) ... OK (0 seconds)
test.IntegerMatrix.diag: (1 checks) ... OK (0 seconds)
test.IntegerVector.matrix.indexing: (3 checks) ... OK (0 seconds)
test.List.column: (1 checks) ... OK (0 seconds)
test.List.row: (1 checks) ... OK (0 seconds)
test.NumericMatrix: (2 checks) ... OK (0 seconds)
test.NumericMatrix.Ctors: (2 checks) ... OK (0 seconds)
test.NumericMatrix.SubMatrix: (1 checks) ... OK (0 seconds)
test.NumericMatrix.colsum: (1 checks) ... OK (0 seconds)
test.NumericMatrix.column: (1 checks) ... OK (0 seconds)
test.NumericMatrix.cumsum: (1 checks) ... OK (0 seconds)
test.NumericMatrix.row: (1 checks) ... OK (0 seconds)
test.NumericMatrix.rowsum: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Module.R 
test.Module: (9 checks) ... OK (6.22 seconds)
test.Module.Constructor: (1 checks) ... OK (5.55 seconds)
test.Module.member: (4 checks) ... OK (5.28 seconds)
test.Module.property: (4 checks) ... OK (5.34 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Module.client.package.R 
test.Module.package: (3 checks) ... OK (41.82 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.RObject.R 
test.RObject.asDouble: (5 checks) ... OK (0 seconds)
test.RObject.asInt: (6 checks) ... OK (0 seconds)
test.RObject.asLogical: (16 checks) ... OK (0.01 seconds)
test.RObject.asRaw: (11 checks) ... OK (0.01 seconds)
test.RObject.asStdString: (6 checks) ... OK (0.01 seconds)
test.RObject.asStdVectorBool: (6 checks) ... OK (0 seconds)
test.RObject.asStdVectorDouble: (5 checks) ... OK (0 seconds)
test.RObject.asStdVectorInt: (5 checks) ... OK (0 seconds)
test.RObject.asStdVectorRaw: (5 checks) ... OK (0 seconds)
test.RObject.asStdVectorString: (6 checks) ... OK (0.01 seconds)
test.RObject.attr: (1 checks) ... OK (0 seconds)
test.RObject.attr.set: (1 checks) ... OK (0 seconds)
test.RObject.attributeNames: (1 checks) ... OK (0 seconds)
test.RObject.hasAttribute: (1 checks) ... OK (0 seconds)
test.RObject.inherits: (3 checks) ... OK (0 seconds)
test.RObject.isNULL: (8 checks) ... OK (0 seconds)
test.RObject.stdsetdouble: (1 checks) ... OK (0 seconds)
test.RObject.stdsetint: (1 checks) ... OK (0 seconds)
test.RObject.stdsetraw: (1 checks) ... OK (0 seconds)
test.RObject.stdsetstring: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.S4.R 
test.RObject.S4methods: (5 checks) ... OK (0.02 seconds)
test.S4: (7 checks) ... OK (3.62 seconds)
test.S4.dotdataslot: (1 checks) ... OK (0.08 seconds)
test.S4.is: (4 checks) ... OK (0.05 seconds)
test.Vector.AttributeProxy.ambiguity: (1 checks) ... OK (0 seconds)
test.Vector.SlotProxy.ambiguity: (1 checks) ... OK (0.04 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.Vector.R 
test.CharacterVector: (1 checks) ... OK (0 seconds)
test.CharacterVector.Dimension.constructor: (3 checks) ... OK (0 seconds)
test.CharacterVector.STRSXP: (1 checks) ... OK (0 seconds)
test.CharacterVector.assign: (2 checks) ... OK (0 seconds)
test.CharacterVector.comma: (1 checks) ... OK (0 seconds)
test.CharacterVector.create: (1 checks) ... OK (0 seconds)
test.CharacterVector.find: (1 checks) ... OK (0 seconds)
test.CharacterVector.iterator: (2 checks) ... OK (0 seconds)
test.CharacterVector.listOf: (1 checks) ... OK (0 seconds)
test.CharacterVector.matrix.indexing: (3 checks) ... OK (0 seconds)
test.CharacterVector.names.indexing: (1 checks) ... OK (0 seconds)
test.CharacterVector.plusequals: (1 checks) ... OK (0 seconds)
test.CharacterVector.range.constructors: (2 checks) ... OK (0 seconds)
test.CharacterVector.reverse: (2 checks) ... OK (0 seconds)
test.ComplexVector: (1 checks) ... OK (0 seconds)
test.ComplexVector.CPLXSXP: (1 checks) ... OK (0 seconds)
test.ComplexVector.INTSXP: (1 checks) ... OK (0 seconds)
test.ComplexVector.REALSXP: (1 checks) ... OK (0 seconds)
test.ComplexVector.binary.operators: (2 checks) ... OK (0 seconds)
test.ExpressionVector: (1 checks) ... OK (0 seconds)
test.ExpressionVector.eval: (1 checks) ... OK (0 seconds)
test.ExpressionVector.eval.env: (1 checks) ... OK (0 seconds)
test.ExpressionVector.parse: (1 checks) ... OK (0 seconds)
test.ExpressionVector.parse.error: (1 checks) ... OK (0 seconds)
test.ExpressionVector.variadic: (1 checks) ... OK (0 seconds)
test.IntegerVector: (1 checks) ... OK (0 seconds)
test.IntegerVector.Dimension.constructor: (3 checks) ... OK (0 seconds)
test.IntegerVector.INTSXP_: (1 checks) ... OK (0 seconds)
test.IntegerVector.clone: (2 checks) ... OK (0 seconds)
test.IntegerVector.comma: (1 checks) ... OK (0 seconds)
test.IntegerVector.create: (1 checks) ... OK (0 seconds)
test.IntegerVector.create.zero: (1 checks) ... OK (0 seconds)
test.IntegerVector.erase: (2 checks) ... OK (0 seconds)
test.IntegerVector.erase2: (2 checks) ... OK (0 seconds)
test.IntegerVector.fill: (1 checks) ... OK (0 seconds)
test.IntegerVector.insert: (2 checks) ... OK (0 seconds)
test.IntegerVector.names.get: (1 checks) ... OK (0 seconds)
test.IntegerVector.names.indexing: (1 checks) ... OK (0 seconds)
test.IntegerVector.names.set: (1 checks) ... OK (0 seconds)
test.IntegerVector.push.back: (2 checks) ... OK (0 seconds)
test.IntegerVector.push.front: (2 checks) ... OK (0 seconds)
test.IntegerVector.range.constructors: (2 checks) ... OK (0 seconds)
test.IntegerVector.zero: (1 checks) ... OK (0 seconds)
test.List: (1 checks) ... OK (0 seconds)
test.List.Dimension.constructor: (3 checks) ... OK (0.01 seconds)
test.List.VECSXP: (1 checks) ... OK (0 seconds)
test.List.create: (1 checks) ... OK (0 seconds)
test.List.erase: (1 checks) ... OK (0 seconds)
test.List.erase.range: (1 checks) ... OK (0 seconds)
test.List.implicit.push.back: (1 checks) ... OK (0 seconds)
test.List.iterator: (1 checks) ... OK (0 seconds)
test.List.matrix.indexing: (3 checks) ... OK (0 seconds)
test.List.name.indexing: (1 checks) ... OK (0 seconds)
test.List.push.back: (1 checks) ... OK (0 seconds)
test.List.push.front: (1 checks) ... OK (0 seconds)
test.List.stdcomplex: (1 checks) ... OK (0 seconds)
test.List.template: (1 checks) ... OK (0 seconds)
test.NumericVector: (1 checks) ... OK (0 seconds)
test.NumericVector.REALSXP: (1 checks) ... OK (0 seconds)
test.NumericVector.import: (1 checks) ... OK (0 seconds)
test.NumericVector.import.transform: (1 checks) ... OK (0 seconds)
test.RawVector: (1 checks) ... OK (0 seconds)
test.RawVector.REALSXP: (1 checks) ... OK (0 seconds)
test.factors: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.XPTr.R 
test.XPtr: (2 checks) ... OK (7.39 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.as.R 
test.as.bool: (4 checks) ... OK (0 seconds)
test.as.deque.int: (1 checks) ... OK (0 seconds)
test.as.double: (4 checks) ... OK (0 seconds)
test.as.int: (4 checks) ... OK (0 seconds)
test.as.list.int: (1 checks) ... OK (0 seconds)
test.as.raw: (4 checks) ... OK (0 seconds)
test.as.string: (1 checks) ... OK (0 seconds)
test.as.vector.bool: (4 checks) ... OK (0 seconds)
test.as.vector.double: (4 checks) ... OK (0 seconds)
test.as.vector.int: (4 checks) ... OK (0 seconds)
test.as.vector.raw: (4 checks) ... OK (0 seconds)
test.as.vector.string: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.client.package.R 
test.client.packageA: (2 checks) ... OK (23.55 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.environments.R 
test.environment.NotAnEnvironment: (3 checks) ... OK (0.01 seconds)
test.environment.Rcpp: (1 checks) ... OK (0 seconds)
test.environment.assign: (6 checks) ... OK (0 seconds)
test.environment.base.env: (1 checks) ... OK (0.01 seconds)
test.environment.bindingIsActive: (3 checks) ... OK (0 seconds)
test.environment.bindingIsLocked: (3 checks) ... OK (0.01 seconds)
test.environment.child: (1 checks) ... OK (0 seconds)
test.environment.constructor.SEXP: (7 checks) ... OK (0.01 seconds)
test.environment.constructor.int: (14 checks) ... OK (0.01 seconds)
test.environment.constructor.stdstring: (3 checks) ... OK (0 seconds)
test.environment.empty.env: (1 checks) ... OK (0 seconds)
test.environment.exists: (3 checks) ... OK (0 seconds)
test.environment.get: (3 checks) ... OK (0 seconds)
test.environment.global.env: (1 checks) ... OK (0 seconds)
test.environment.isLocked: (5 checks) ... OK (0 seconds)
test.environment.lockBinding: (2 checks) ... OK (0 seconds)
test.environment.ls: (4 checks) ... OK (0 seconds)
test.environment.namespace.env: (2 checks) ... OK (0.01 seconds)
test.environment.parent: (2 checks) ... OK (0 seconds)
test.environment.remove: (5 checks) ... OK (0.01 seconds)
test.environment.square: (1 checks) ... OK (0 seconds)
test.environment.unlockBinding: (2 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.macros.R 
test.RCPPFUNCTION: (4 checks) ... OK (8.52 seconds)
test.RCPPFUNCTION.VOID: (10 checks) ... OK (7.56 seconds)
test.RCPPXPFIELD: (8 checks) ... OK (4.04 seconds)
test.RCPPXPMETHOD: (18 checks) ... OK (17.41 seconds)
test.long.long: (1 checks) ... OK (3.75 seconds)
test.macro.switch: (8 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.misc.R 
test.Argument: (1 checks) ... OK (0 seconds)
test.Dimension.const: (1 checks) ... OK (0 seconds)
test.Symbol: (4 checks) ... OK (0 seconds)
test.Symbol.notcompatible: (6 checks) ... OK (0.01 seconds)
test.evaluator.error: (1 checks) ... OK (0 seconds)
test.evaluator.ok: (1 checks) ... OK (0 seconds)
test.exceptions: (7 checks) ... OK (0 seconds)
test.has.iterator: (7 checks) ... OK (3.68 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.modref.R 
test.modRef: (0 checks) ... OK (5.16 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.stats.R 
test.stats.dbeta: (1 checks) ... OK (0 seconds)
test.stats.dbinom: (1 checks) ... OK (0 seconds)
test.stats.dgamma: (1 checks) ... OK (0 seconds)
test.stats.dnorm: (1 checks) ... OK (0 seconds)
test.stats.dpois: (1 checks) ... OK (0 seconds)
test.stats.dt: (1 checks) ... OK (0 seconds)
test.stats.dunif: (1 checks) ... OK (0 seconds)
test.stats.pbeta: (3 checks) ... OK (0 seconds)
test.stats.pbinom: (1 checks) ... OK (0 seconds)
test.stats.pgamma: (1 checks) ... OK (0 seconds)
test.stats.pnorm: (4 checks) ... OK (0.01 seconds)
test.stats.ppois: (1 checks) ... OK (0 seconds)
test.stats.pt: (1 checks) ... OK (0 seconds)
test.stats.punif: (1 checks) ... OK (0 seconds)
test.stats.qbinom: (1 checks) ... OK (0 seconds)
test.stats.qnorm: (4 checks) ... OK (0 seconds)
test.stats.qpois.prob: (1 checks) ... OK (0 seconds)
test.stats.qt: (4 checks) ... OK (0 seconds)
test.stats.qunif: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.sugar.R 
test.sugar.Range: (1 checks) ... OK (0 seconds)
test.sugar.abs: (1 checks) ... OK (0 seconds)
test.sugar.all.equal: (5 checks) ... OK (0 seconds)
test.sugar.all.greater: (5 checks) ... OK (0 seconds)
test.sugar.all.greater.or.equal: (5 checks) ... OK (0 seconds)
test.sugar.all.less: (4 checks) ... OK (0 seconds)
test.sugar.all.less.or.equal: (5 checks) ... OK (0 seconds)
test.sugar.all.not.equal: (5 checks) ... OK (0 seconds)
test.sugar.all.one.equal: (5 checks) ... OK (0 seconds)
test.sugar.all.one.greater: (5 checks) ... OK (0 seconds)
test.sugar.all.one.greater.or.equal: (6 checks) ... OK (0 seconds)
test.sugar.all.one.less: (5 checks) ... OK (0 seconds)
test.sugar.all.one.less.or.equal: (6 checks) ... OK (0 seconds)
test.sugar.all.one.not.equal: (5 checks) ... OK (0 seconds)
test.sugar.any.equal: (5 checks) ... OK (0 seconds)
test.sugar.any.equal.not: (5 checks) ... OK (0 seconds)
test.sugar.any.greater: (4 checks) ... OK (0 seconds)
test.sugar.any.greater.or.equal: (5 checks) ... OK (0 seconds)
test.sugar.any.isna: (1 checks) ... OK (0 seconds)
test.sugar.any.less: (4 checks) ... OK (0 seconds)
test.sugar.any.less.or.equal: (5 checks) ... OK (0 seconds)
test.sugar.any.not.equal: (5 checks) ... OK (0 seconds)
test.sugar.assignment: (4 checks) ... OK (0 seconds)
test.sugar.asvector: FAILURE !! (check number 2)
Error in checkEquals(res[[2]], as.vector(outer(1:4, 1:5, "+"))) : 
  Mean absolute difference: 5.5
test.sugar.beta: FAILURE !! (check number 1)
Error in checkEquals(fx(10:6, 5:1), list(VV = beta(10:6, 5:1), PV = beta(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
test.sugar.ceil: (1 checks) ... OK (0 seconds)
test.sugar.choose: FAILURE !! (check number 1)
Error in checkEquals(fx(10:6, 5:1), list(VV = choose(10:6, 5:1), PV = choose(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
test.sugar.complex: (1 checks) ... OK (0.01 seconds)
test.sugar.constructor: (4 checks) ... OK (0 seconds)
test.sugar.cumsum: (2 checks) ... OK (0 seconds)
test.sugar.diag: FAILURE !! (check number 1)
Error in checkEquals(res, target) : 
  Component 3: Mean absolute difference: 5
test.sugar.diff: (1 checks) ... OK (0 seconds)
test.sugar.divides: (1 checks) ... OK (0 seconds)
test.sugar.exp: (1 checks) ... OK (0 seconds)
test.sugar.floor: (1 checks) ... OK (0 seconds)
test.sugar.gamma: (1 checks) ... OK (0 seconds)
test.sugar.head: (1 checks) ... OK (0 seconds)
test.sugar.ifelse: (1 checks) ... OK (0 seconds)
test.sugar.isna: (1 checks) ... OK (0 seconds)
test.sugar.isna.isna: (1 checks) ... OK (0 seconds)
test.sugar.lapply: (1 checks) ... OK (0 seconds)
test.sugar.lbeta: FAILURE !! (check number 1)
Error in checkEquals(fx(10:6, 5:1), list(VV = lbeta(10:6, 5:1), PV = lbeta(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
test.sugar.lchoose: FAILURE !! (check number 1)
Error in checkEquals(fx(10:6, 5:1), list(VV = lchoose(10:6, 5:1), PV = lchoose(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
test.sugar.log1p: (1 checks) ... OK (0 seconds)
test.sugar.matrix.outer: FAILURE !! (check number 1)
Error in checkEquals(fx(x, y), outer(x, y, "+")) : 
  Mean absolute difference: 4.5
test.sugar.matrix.row: (1 checks) ... OK (0 seconds)
test.sugar.minus: (1 checks) ... OK (0 seconds)
test.sugar.plus: (1 checks) ... OK (0 seconds)
test.sugar.plus.all: (1 checks) ... OK (0 seconds)
test.sugar.plus.seqlen: (1 checks) ... OK (0 seconds)
test.sugar.pmax: (1 checks) ... OK (0 seconds)
test.sugar.pmax.one: (1 checks) ... OK (0 seconds)
test.sugar.pmin: (1 checks) ... OK (0.01 seconds)
test.sugar.pmin.one: (1 checks) ... OK (0 seconds)
test.sugar.pow: (1 checks) ... OK (0 seconds)
test.sugar.psigamma: FAILURE !! (check number 1)
Error in checkEquals(fx(10:6, 5:1), list(VV = psigamma(10:6, 5:1), PV = psigamma(10,  : 
  Component 1: Numeric: lengths (0, 5) differ
Component 2: Numeric: lengths (0, 5) differ
Component 3: Numeric: lengths (0, 5) differ
test.sugar.rep: (1 checks) ... OK (0 seconds)
test.sugar.rev: (1 checks) ... OK (0 seconds)
test.sugar.sapply: (1 checks) ... OK (0 seconds)
test.sugar.sapply.list: (1 checks) ... OK (0 seconds)
test.sugar.sapply.rawfun: (1 checks) ... OK (0.01 seconds)
test.sugar.sapply.square: (1 checks) ... OK (0 seconds)
test.sugar.seqlaong: (1 checks) ... OK (0 seconds)
test.sugar.seqlen: (1 checks) ... OK (0 seconds)
test.sugar.sign: (1 checks) ... OK (0 seconds)
test.sugar.sum: (2 checks) ... OK (0 seconds)
test.sugar.tail: (1 checks) ... OK (0 seconds)
test.sugar.times: (1 checks) ... OK (0.02 seconds)
test.sugar.unary.minus: (2 checks) ... OK (0 seconds)
test.sugar.wrap: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.support.R 
test.divides.REALSXP: (1 checks) ... OK (0 seconds)
test.functions.REALSXP: (1 checks) ... OK (0 seconds)
test.minus.REALSXP: (1 checks) ... OK (0 seconds)
test.plus.REALSXP: (1 checks) ... OK (0 seconds)
test.times.REALSXP: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /tmp/Rcpp.Rcheck/Rcpp/unitTests/runit.wrap.R 
test.wrap.map.string.Rbyte: (1 checks) ... OK (0 seconds)
test.wrap.map.string.bool: (1 checks) ... OK (0 seconds)
test.wrap.map.string.double: (1 checks) ... OK (0 seconds)
test.wrap.map.string.generic: (1 checks) ... OK (0 seconds)
test.wrap.map.string.int: (1 checks) ... OK (0 seconds)
test.wrap.map.string.string: (1 checks) ... OK (0 seconds)
test.wrap.multimap.string.Rbyte: (1 checks) ... OK (0 seconds)
test.wrap.multimap.string.bool: (1 checks) ... OK (0 seconds)
test.wrap.multimap.string.double: (1 checks) ... OK (0 seconds)
test.wrap.multimap.string.generic: (1 checks) ... OK (0 seconds)
test.wrap.multimap.string.int: (1 checks) ... OK (0 seconds)
test.wrap.multimap.string.string: (1 checks) ... OK (0 seconds)
test.wrap.unordered.map.string.Rbyte: (3 checks) ... OK (0 seconds)
test.wrap.unordered.map.string.bool: (3 checks) ... OK (0 seconds)
test.wrap.unordered.map.string.double: (3 checks) ... OK (0 seconds)
test.wrap.unordered.map.string.generic: (3 checks) ... OK (0 seconds)
test.wrap.unordered.map.string.int: (3 checks) ... OK (0 seconds)
test.wrap.unordered.map.string.string: (3 checks) ... OK (0 seconds)

  
  


  


      

    

    

      
      

        


  

        

      Jan de Leeuw
    

    

      
      #
    

  


  

      
Yes, well, this still does not explain why Doug gets the same error
on Ubuntu.

        
On Apr 29, 2011, at 07:23 , Conrad Sanderson wrote:

        

            

      
      
      
    

        
===
Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics;
Director: UCLA Center for Environmental Statistics (CES);
Editor: Journal of Multivariate Analysis, Journal of Statistical Software;
US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw at stat.ucla.edu
.mac: jdeleeuw ++++++  aim: deleeuwjan ++++++ skype: j_deleeuw
homepages: http://gifi.stat.ucla.edu ++++++ http://www.cuddyvalley.org
 -------------------------------------------------------------------------------------------------
          No matter where you go, there you are. --- Buckaroo Banzai
                   http://gifi.stat.ucla.edu/sounds/nomatter.au                                  
 -------------------------------------------------------------------------------------------------

  
  


  


      

    

    

      
      

        


  

        

      Douglas Bates
    

    

      
      #
    

  


  

      
OK, this is bizarre.  I am able to install the RcppArmadillo package
on my current setup provided that I turn on optimization in the call
to g++ to compile RcppArmadillo.cpp.  The only difference between the
following two calls is the -O3 flag.  (I haven't tried other levels of
optimization yet but presumably it would work with -O and -O2).
Compare the following

bates at bates3:/tmp$ R CMD INSTALL RcppArmadillo_0.2.19.1.tar.gz
* installing to library ?/home/bates/R/x86_64-unknown-linux-gnu-library/2.13?
* installing *source* package ?RcppArmadillo? ...
** libs
g++ -I/usr/share/R/include
-I"/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/include"
-I../inst/include -fpic  -g -O3 -Wall -pipe -pedantic -c
RcppArmadillo.cpp -o RcppArmadillo.o
g++ -I/usr/share/R/include
-I"/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/include"
-I../inst/include -fpic  -g -O3 -Wall -pipe -pedantic -c fastLm.cpp -o
fastLm.o
g++ -shared -o RcppArmadillo.so RcppArmadillo.o fastLm.o
-L/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/lib -lRcpp
-Wl,-rpath,/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/lib
-llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
installing to /home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (RcppArmadillo)
bates at bates3:/tmp$ R CMD INSTALL RcppArmadillo_0.2.19.1.tar.gz
* installing to library ?/home/bates/R/x86_64-unknown-linux-gnu-library/2.13?
* installing *source* package ?RcppArmadillo? ...
** libs
g++ -I/usr/share/R/include
-I"/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/include"
-I../inst/include -fpic  -g -Wall -pipe -pedantic -c RcppArmadillo.cpp
-o RcppArmadillo.o
g++ -I/usr/share/R/include
-I"/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/include"
-I../inst/include -fpic  -g -Wall -pipe -pedantic -c fastLm.cpp -o
fastLm.o
g++ -shared -o RcppArmadillo.so RcppArmadillo.o fastLm.o
-L/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/lib -lRcpp
-Wl,-rpath,/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/Rcpp/lib
-llapack -lblas -lgfortran -lm -L/usr/lib64/R/lib -lR
installing to /home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs/RcppArmadillo.so':
  /home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo/libs/RcppArmadillo.so:
undefined symbol: _ZN4arma12arma_version5majorE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ?/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo?
* restoring previous
?/home/bates/R/x86_64-unknown-linux-gnu-library/2.13/RcppArmadillo?

        
On Fri, Apr 29, 2011 at 9:32 AM, Jan de Leeuw <deleeuw at stat.ucla.edu> wrote:

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jan de Leeuw
    

    

      
      #
    

  


  

      
Interesting. Stabilizing a compile by using the optimization flags. The runs I reported
earlier (with Apple's g++-4.2, Apple's llvm g++-4.2, and g++-4.7 from svn)
all used the -O4 flag. Although the symptoms are the same as mine, it seems
the disease is different.

        
On Apr 29, 2011, at 09:59 , Douglas Bates wrote:

        

            

      
      
      
    

        
====================================================================
    Jan de Leeuw, 11667 Steinhoff Rd, Frazier Park, CA 93225
    home 661-245-1725 mobile 661-231-5416 work 310-825-9550
    .mac: jdeleeuw +++  aim: deleeuwjan +++ skype: j_deleeuw
====================================================================
If I wanted you to understand it, I would have explained it better.
                                                -- Johan Cruijff                                 
====================================================================

  
  


  


      

    

    

      
      

        


  

        

      Douglas Bates
    

    

      
      #
    

  


  

      
And I can get past R CMD check Rcpp if I include -O3 in CXXFLAGS.

        
On Fri, Apr 29, 2011 at 11:59 AM, Douglas Bates <bates at stat.wisc.edu> wrote: